Hi Yuqi,
Average-precision for the positive-unlabeled provides a relative number. Average-precision generally cannot be compared between different training parameters, and not compared to any absolute value.
Generally, it should gradually increase like your plots show. But in the end, models should be compared by how many good particles are picked and how many orientations are picked.
So, your plots look fine. But you should check the models by going through 2D/3D classification and 3D refinement.
Best,
-Alex